>TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent the RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.

Probab=99.59 E-value=9.8e-14 Score=111.32 Aligned_cols=190 Identities=18% Similarity=0.255 Sum_probs=142.1 Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998 Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302) Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302) T Consensus 8 ~~~~~~~-~G~~~a~~~~i~~y~~fv~ak~~~yfl~Gad~edi~qeGmiGlyka~rd~~~~~l~sf~afaelC~trqiit 86 (198) T TIGR02859 8 EIVELAR-EGDEKALEYLIEKYKNFVKAKARSYFLVGADKEDIIQEGMIGLYKAIRDYKEDKLSSFKAFAELCVTRQIIT 86 (198) T ss_pred HHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999997-011889999999999998775311013206456566611689999997531567899999999999999999 Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234 Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302) Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302) T Consensus 87 aiktatrqkhiP----------------------------------------------------ln~y~sl~kPiy~~-~ 113 (198) T TIGR02859 87 AIKTATRQKHIP----------------------------------------------------LNSYVSLNKPIYDE-E 113 (198) T ss_pred HHHHHHHHCCCC----------------------------------------------------CHHHEECCCCCCCC-C T ss_conf 988765202465----------------------------------------------------20000025652545-2 Q ss_pred CCCCHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 5320000012356-870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 196 ~~~~~~d~l~~~~-~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 114 sdrtl~d~~~~~~~~dP~~l~i~~e~~~~~~~~~~~~---ls~le~~vl~~yl---~G~~yqei~~~l~r~~ksi----d 183 (198) T TIGR02859 114 SDRTLLDVVSEAKVADPEELIISKEEYEKIESKLEEL---LSDLELKVLVLYL---DGKSYQEIAEDLNRHVKSI----D 183 (198) T ss_pred CHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH---CCCHHHHHHHHHHHHHHHH----H T ss_conf 0147999885443225277763168899999999999---9999999999984---5740788998864566789----9 Q ss_pred HHHHHHHHHHHHHHC Q ss_conf 999999999997401 Q gi|254780611|r 275 RAFKKVQESIQKQVE 289 (302) Q Consensus 275 ~AL~kLR~~l~~~~~ 289 (302) T Consensus 184 nalqrvkrkle~~l~ 198 (198) T TIGR02859 184 NALQRVKRKLEKYLE 198 (198) T ss_pred HHHHHHHHHHHHHCC T ss_conf 999999999976309

HHsearch alignment for GI: 254780611 and conserved domain: TIGR02859